Variant report

Variant	rs3783315
Chromosome Location	chr14:35337365-35337366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35330584..35332692-chr14:35335124..35338099,2	MCF-7	breast:
2	chr14:35336064..35338537-chr2:43453316..43454844,2	MCF-7	breast:
3	chr14:35329109..35331182-chr14:35336949..35340434,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198604	Chromatin interaction
ENSG00000152518	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10136352	0.81[JPT][hapmap]
rs10150083	0.83[JPT][hapmap]
rs11847610	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200414	0.81[JPT][hapmap]
rs12431818	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12432567	0.86[ASN][1000 genomes]
rs12433706	0.89[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs12435778	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12435859	0.84[AFR][1000 genomes]
rs12586459	0.98[ASN][1000 genomes]
rs12586462	0.86[ASN][1000 genomes]
rs12587021	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587251	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12587390	0.81[CHB][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12587913	1.00[ASN][1000 genomes]
rs12588318	0.83[ASN][1000 genomes]
rs12590112	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs12590268	0.96[ASN][1000 genomes]
rs1400745	0.90[JPT][hapmap]
rs17102726	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17102768	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17102795	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17102829	0.90[JPT][hapmap]
rs17526787	0.96[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs17526884	0.87[AFR][1000 genomes]
rs1959154	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2295468	0.96[ASN][1000 genomes]
rs2383675	0.88[LWK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2383676	0.86[ASN][1000 genomes]
rs2383677	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap]
rs34072166	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34245772	0.96[ASN][1000 genomes]
rs3783316	0.81[JPT][hapmap]
rs5016735	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55979964	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58268256	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs58587072	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59092668	0.81[AFR][1000 genomes]
rs59678582	0.84[AFR][1000 genomes]
rs61981198	0.84[ASN][1000 genomes]
rs61981200	0.85[ASN][1000 genomes]
rs61981202	0.86[ASN][1000 genomes]
rs61981204	0.80[ASN][1000 genomes]
rs61981228	0.86[ASN][1000 genomes]
rs61981232	0.88[ASN][1000 genomes]
rs61981234	0.93[ASN][1000 genomes]
rs61981236	0.93[ASN][1000 genomes]
rs61981237	0.93[ASN][1000 genomes]
rs61988010	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61988011	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61988012	0.95[ASN][1000 genomes]
rs61988013	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61988044	1.00[ASN][1000 genomes]
rs61988045	0.98[ASN][1000 genomes]
rs7142012	1.00[ASN][1000 genomes]
rs7148400	0.81[JPT][hapmap]
rs7150069	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7153289	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs7155348	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8005470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005659	0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap]
rs8010504	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8010579	0.81[CHB][hapmap]
rs8013484	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv976829	chr14:35332947-35341310	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3783315	SCFD1	cis	cerebellum	SCAN
rs3783315	SNX6	cis	parietal	SCAN
rs3783315	NUBPL	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35269400-35341600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr14:35276200-35342400	Weak transcription	Pancreas	Pancrea
3	chr14:35312800-35341400	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:35312800-35341600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:35312800-35341600	Weak transcription	Psoas Muscle	Psoas
6	chr14:35312800-35342200	Weak transcription	Small Intestine	intestine
7	chr14:35312800-35342400	Weak transcription	Left Ventricle	heart
8	chr14:35313600-35341600	Weak transcription	Brain Germinal Matrix	brain
9	chr14:35318400-35342200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr14:35321800-35342400	Weak transcription	Gastric	stomach
11	chr14:35322600-35341400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr14:35322800-35341200	Weak transcription	HSMMtube	muscle
13	chr14:35322800-35342200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr14:35323200-35341800	Weak transcription	NHLF	lung
15	chr14:35323800-35342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:35324600-35341600	Weak transcription	Fetal Lung	lung
17	chr14:35324600-35342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr14:35324800-35342200	Weak transcription	Ovary	ovary
19	chr14:35327000-35341600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:35327000-35342400	Weak transcription	Esophagus	oesophagus
21	chr14:35327200-35342400	Weak transcription	Spleen	Spleen
22	chr14:35327400-35338600	Weak transcription	K562	blood
23	chr14:35327600-35341200	Weak transcription	Thymus	Thymus
24	chr14:35327600-35341400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr14:35327800-35341600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:35328400-35337400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr14:35329600-35337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr14:35329600-35338200	Weak transcription	Fetal Thymus	thymus
29	chr14:35329600-35342200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr14:35330000-35341400	Weak transcription	Fetal Intestine Large	intestine
31	chr14:35330000-35341600	Weak transcription	Fetal Intestine Small	intestine
32	chr14:35330000-35341600	Weak transcription	Fetal Stomach	stomach
33	chr14:35331200-35340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr14:35331200-35341200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr14:35331200-35341400	Weak transcription	NHDF-Ad	bronchial
36	chr14:35331200-35341600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr14:35331200-35341600	Weak transcription	Placenta	Placenta
38	chr14:35331200-35341800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr14:35331200-35341800	Weak transcription	Osteobl	bone
40	chr14:35331200-35342000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:35331200-35342200	Weak transcription	Fetal Brain Female	brain
42	chr14:35331400-35338400	Weak transcription	HMEC	breast
43	chr14:35331400-35338600	Weak transcription	Primary B cells from cord blood	blood
44	chr14:35331400-35338600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:35331400-35338800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr14:35331400-35338800	Weak transcription	HSMM	muscle
47	chr14:35331400-35341200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr14:35331400-35341200	Weak transcription	Adipose Nuclei	Adipose
49	chr14:35331400-35341400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr14:35331400-35341600	Weak transcription	Rectal Mucosa Donor 29	rectum

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